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9xau

Glyoxysomal Citrate Synthase 3 from Arabidopsis thaliana in complex with OAA

Method: X-RAY DIFFRACTION D_max: 125.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xau
deposition_date	2025-10-23
title	Glyoxysomal Citrate Synthase 3 from Arabidopsis thaliana in complex with OAA
keywords	citrate synthase, glyoxysome, glyoxylate cycle, Arabidopsis, TRANSFERASE; TRANSFERASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	38.73 Å
rg_electron	38.25 Å
i0	536851000.00
molecular_weight	194050.0 kDa
excluded_volume	244750 Å³
envelope_volume	306730 Å³
shell_volume	64610 Å³
envelope_diameter	128.8 Å
shell_rg	45.61 Å
envelope_rg	38.27 Å
shape_rg	38.24 Å
total_rg	38.66 Å
total_atoms	13685
n_residues	1744
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	125.5 Å
rg_real	38.66 Å
rg_real_error	0.89 Å
i0_real	5.3680e+08
i0_real_error	8.4360e+06
rg_reciprocal	38.71 Å
i0_reciprocal	536900000.0000
total_estimate	0.8834
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	42.9 Å
skewness	0.308
kurtosis	-0.405
angular_range	— – 0.2050 Å⁻¹
current_alpha	0.0000
highest_alpha	196100000.0000
n_real_points	42
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.783

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Citrate synthase 3, peroxisomal
formula_weight	52786.2 kDa
ec_number	2.3.3.16
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	14111

GPLGSDTSVAPLGSLKGTLTIVDERTGKNYKVPVSDDGTVKAVDFKKIVTGKEDKGLKLYDPGYLNTAPVRSSISYIDGDEGILRYRGYPIEEMAENSTFLEVAYLLMYGNLPSESQLSDWEFAVSQHSAVPQGVLDIIQSMPHDAHPMGVLVSAMSALSIFHPDANPALRGQDIYDSKQVRDKQIIRIIGKAPTIAAAAYLRMAGRPPVLPSGNLPYADNFLYMLDSLGNRSYKPNPRLARVLDILFILHAEHEMNCSTAAARHLASSGVDVYTAVAGAVGALYGPLHGGANEAVLKMLSEIGTVENIPEFIEGVKNRKRKMSGFGHRVYKNYDPRAKVIKNLADEVFSIVGKDPLIEVAVALEKAALSDDYFVKRKLYPNVDFYSGLIYRAMGFPPEFFTVLFAIPRMAGYLSHWKESLDDPDTKIMRPQQVYTGVWLRHYTPVRERIVTDDSKESDKLGQVATSNASRRRLAGSSV

Source

organism	Arabidopsis thaliana
common_name	thale cress
ncbi_taxonomy_id	3702
host_organism	Escherichia coli

Entity 2 non-polymer

description	OXALOACETATE ION
formula_weight	131.1 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	426

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6. Citations (1)

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length_a	79.084 Å
length_b	64.726 Å
length_c	192.512 Å
angle_alpha	90.00 °
angle_beta	92.62 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.950 Å
resolution_low	48.100 Å
r_factor	—
r_work	0.1860
r_free	0.2250

fit	/app/data/saxs_computation/xa/9xau/9xau.fit
pddf	/app/data/pr_computation/xa/9xau/9xau.pr.out
profile	/app/data/saxs_computation/xa/9xau/9xau.dat

Glyoxysomal Citrate Synthase 3 from Arabidopsis thaliana in complex with OAA

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction